Etan Patz’s alleged killer tried to confess to cops years ago that he had murdered the long-missing 6-year-old — but he was dismissed as a nutjob and detectives never followed through, the suspect’s sister told The Post yesterday.

“Every time the anniversary of that little boy came up on TV, I would say, ‘Why doesn’t he turn himself in?’ ” recalled Lucy Suarez, 43, the youngest sister of Pedro Hernandez.

“And my sister said, ‘He did, but the police let him go because they said he was too crazy,’ ” Suarez said.

Sources yesterday also revealed that five days after Etan disappeared, cops saw Hernandez at the bodega, where one of the owners explained away his presence by noting he was merely his brother-in-law. There is no record that police ever interviewed Hernandez that day about Etan.

Hernandez, 51, confessed to the NYPD Wednesday after a relative ratted him out, police said. He was arraigned on a second-degree murder charge from Bellevue Hospital on the 33rd anniversary of Etan’s disappearance.

“Every time the Patz anniversary came up, and we saw it on TV, we would always get haunted by it,” Suarez said from her home in Camden, NJ.

“I would say, ‘Damn, this thing isn’t dying down. That little boy’s blood is crying out for mercy.’ And we would pray, we would pray for God’s mercy, so God must have heard us.”

Cops yesterday denied that Hernandez ever confessed to killing Patz any time before Wednesday.

“I figured you’d be coming for me because the anniversary was coming up,” the married dad said, according to sources. “I’ll tell you everything you need to know about Etan Patz.”

He then wept, repeatedly saying he was sorry as he confessed how he used the promise of a cold soda to lure Etan from the corner of West Broadway and Prince Street, then strangled him from behind in the basement of the bodega at 448 West Broadway.

He then bagged up the boy’s corpse, placed the bag in a box and dumped the box under some trash next to 113 Thompson St., he said.

The fact that Hernandez is so “lucid” and “compelling” in his confession video is the reason prosecutors pushed forward with the case, a law enforcement source said.

Hernandez moved to New Jersey a short time later. He told family members and people at a religious retreat, “I did a bad thing. I killed a boy in New York.”

His wife and daughter traveled from Maple Shade, NJ, but left Manhattan Criminal Court before his arraignment.

Hernandez, who cops and family members said has HIV, was taken to Bellevue yesterday after threatening to kill himself, sources said. He was arraigned via a video link to a courtroom.

“The defendant is schizophrenic and bipolar. He’s under medication, and he was admitted [to Bellevue] initially because of the medications he was on,” said Hernandez’s lawyer, Harvey Fishbein. “There is also a history of hallucinations, both visual and auditory.”

Hernandez, who did not enter a plea, was ordered held without bond, and a psychiatric evaluation was ordered by Justice Matthew Sciarrino.